An increasing number of human immunodeficiency virus (HIV)-infected patients are achieving virologic suppression on antiretroviral therapy (ART) limiting the use of primary and secondary antimicrobial prophylaxis. However, in low-income and resource-limited settings, half of those infected with HIV are unaware of their diagnosis, and fewer than 50% of patients on ART achieve virologic suppression. Management of comorbidities and opportunistic infections among patients on ART may lead to inevitable drug-drug interactions (DDIs) and even toxicities. Elderly patients, individuals with multiple comorbidities, those receiving complex ART, and patients living in low-income settings experience higher rates of DDIs. Management of these cytochrome P450-mediated, nonmediated, and drug transport system DDIs is critical in HIV-infected patients, particularly those in resource-limited settings with few options for ART. This article critically analyzes and provides recommendations to manage significant DDIs and drug toxicities in HIV-infected patients receiving ART.